I am upgrading from a Motorguide Pro Series 75 to a Motorguide Tour Pro. Was wondering if there is a huge difference in foot pedal size? I have a foot pedal recess already in my boat that came from the factory. Its carpeted over so if I have to enlarge the recess I'm going to have to pull up tge carpet. Never done that and didn't know how big of a deal it is.

Why would you have to pull carpet?  If you need a bigger tray take out your current tray, mark your pattern, and cut the carpet while cutting the deck. 

If you have to pull the carpet, lacquer thinner should loosen the glue so you can take it back then replace it when you are ready.

The carpet is laid over my current foot pedal recess tray. I wasn't sure if I needed to pull the carpet up to remove the current tray and cut the hole for the new one?

you shouldn’t have to pull up your carpet. you should get a paper template with your new recess tray. simply trace it out and use a razor knife to remove only the desired piece of carpet, drill holes at the corners and a jig saw or multi tool to cut out the decking and old recess tray. piece of cake. some decent youtubes out there too.